<?xml version="1.0"?>
<tool id="delete_features" name="Delete all annotations from an Apollo record" version="1.6" profile="16.04">
  <description></description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <code file="webapollo.py"/>
  <command detect_errors="aggressive"><![CDATA[
#if str($ask_one) == "yes":
	## Nope, still don't trust them to not be dumb (or malicious), so we backup first.
	python $__tool_directory__/export.py
	@ADMIN_AUTH@
	@ORG_OR_GUESS@
	--gff "$gff_out"
	--fasta "$fasta_out"
	--json "$json_out"
    "$__user_email__"

    &&

	## Now we delete
	python $__tool_directory__/delete_features.py
	@ADMIN_AUTH@
	@ORG_OR_GUESS@
	"$__user_email__"
	#if str($filter) != "all"
		--type $filter
	#end if
	> $output;
#else
    echo "Nothing to do" > $output;
#end if
    ]]></command>
  <inputs>
    <expand macro="org_or_guess" />
    <param name="filter" type="select" label="Feature Type Filter">
        <option value="all">All</option>
        <option value="mRNA">Genes</option>
        <option value="terminator">Terminators</option>
        <option value="tRNA">tRNAs</option>
    </param>
    <param name="ask_one" type="boolean" truevalue="yes" falsevalue="" label="Are you SURE you want to do this?" help="It will PERMANENTLY delete all of the features on this organism."/>
  </inputs>
  <outputs>
    <data format="tabular" name="output" label="Process and Error Log">
        <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
    </data>

    <data format="gff3" name="gff_out" label="Annotations from Apollo" hidden="true"/>
    <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo" hidden="true"/>
    <data format="json" name="json_out" label="Metadata from Apollo" hidden="true"/>
  </outputs>
  <tests>
      <test expect_failure="true">
          <conditional name="org_source">
              <param name="source_select" value="direct"/>
              <param name="org_raw" value="Test org" />
          </conditional>
          <param name="filter" value="all"/>
          <param name="ask_one" value="yes"/>
          <expand macro="test_result" />
      </test>
  </tests>
  <help><![CDATA[
**What it does**

Deletes every single one of the annotations on an organism. Intentionally.

**Why?**

There are legitimate uses for this tool, generally re-opened genomes is a good
one. Needing to transfer annotations from one build of an organism to another
(with the same refseq name).


@REFERENCES@
]]></help>
  <expand macro="citations"/>
</tool>